Genetic Variant NUBP2:c.*121C>G (chr16-1788835-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012225.4(NUBP2):c.*121C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 1,286,368 control chromosomes in the GnomAD database, including 303,674 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.70 ( 37770 hom., cov: 34)

Exomes 𝑓: 0.68 ( 265904 hom. )

Consequence

NUBP2
NM_012225.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.04

Publications

50 publications found

Variant links:

Genes affected

NUBP2 (HGNC:8042): (NUBP iron-sulfur cluster assembly factor 2, cytosolic) This gene encodes an adenosine triphosphate (ATP) and metal-binding protein that is required for the assembly of cyotosolic iron-sulfur proteins. The encoded protein functions in a heterotetramer with nucleotide-binding protein 1 (NUBP1). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2013]

NUBP2 links:

SPSB3 (HGNC:30629): (splA/ryanodine receptor domain and SOCS box containing 3) Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be located in cytosol. Predicted to be part of SCF ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

SPSB3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUBP2	NM_012225.4 link	c.*121C>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000262302.14	NP_036357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUBP2	ENST00000262302.14 link	c.*121C>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_012225.4	ENSP00000262302.9

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

106667

AN:

152022

Hom.:

37741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.781

Gnomad AMI

AF:

0.816

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.739

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.586

Gnomad FIN

AF:

0.563

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.690

Gnomad OTH

AF:

0.714

GnomAD4 exome

AF:

0.682

AC:

773558

AN:

1134228

Hom.:

265904

Cov.:

AF XY:

0.678

AC XY:

375219

AN XY:

553424

show subpopulations

African (AFR)

AF:

0.787

AC:

19649

AN:

24966

American (AMR)

AF:

0.708

AC:

13616

AN:

19230

Ashkenazi Jewish (ASJ)

AF:

0.728

AC:

12989

AN:

17846

East Asian (EAS)

AF:

0.485

AC:

16096

AN:

33162

South Asian (SAS)

AF:

0.564

AC:

31968

AN:

56646

European-Finnish (FIN)

AF:

0.579

AC:

17604

AN:

30390

Middle Eastern (MID)

AF:

0.702

AC:

2633

AN:

3752

European-Non Finnish (NFE)

AF:

0.696

AC:

625852

AN:

899820

Other (OTH)

AF:

0.685

AC:

33151

AN:

48416

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

11434

22869

34303

45738

57172

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16064

32128

48192

64256

80320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.702

AC:

106748

AN:

152140

Hom.:

37770

Cov.:

AF XY:

0.692

AC XY:

51498

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.781

AC:

32419

AN:

41530

American (AMR)

AF:

0.699

AC:

10702

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.739

AC:

2566

AN:

3472

East Asian (EAS)

AF:

0.562

AC:

2895

AN:

5152

South Asian (SAS)

AF:

0.584

AC:

2817

AN:

4822

European-Finnish (FIN)

AF:

0.563

AC:

5965

AN:

10604

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.690

AC:

46904

AN:

67940

Other (OTH)

AF:

0.716

AC:

1513

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1671

3341

5012

6682

8353

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

820

1640

2460

3280

4100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.579

Hom.:

1532

Bravo

AF:

0.722

Asia WGS

AF:

0.574

AC:

1999

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.34

(source)

DANN

Benign

0.44

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over